wp-cli is not working properly. No response from commands

I am trying to make a copy of a live site on a test server. I installed wp-cli and wp-cli sometimes works and sometimes doesn’t. When it doesn’t work, it just returns nothing. Not one character of output. I can view the website, apache, php and mysql all seem to be working. I turned on WP_DEBUG in wp-config.php and I see a couple of minor errors, as follows:

PHP Notice: wpdb::escape is deprecated since version
3.6! Use wpdb::prepare() or esc_sql() instead. in /var/www/wp-includes/functions.php on line 3083 Notice: wpdb::escape
is deprecated since version 3.6! Use wpdb::prepare()
or esc_sql() instead. in /var/www/wp-includes/functions.php on line
3083

I have tried wp-cli --debug

The only command that works is wp-cli --info

This is the output of wp-cli, in case that is helpful.

PHP binary: /usr/bin/php5‌‌
PHP version: 5.5.3-1ubuntu2.3
php.ini used: /etc/php5/cli/php.ini
WP-CLI root dir: phar://wp-cli.phar
WP-CLI global config:
WP-CLI project config:
WP-CLI version: 0.15.0

Every once in a while, a command will work. This is very strange.

You need to use the –url flag when you have a multisite.

wp-cli --debug --url=www.example.com

or

wp theme list --url=www.example.com